library(knitr)
packageVersion("knitr")
## [1] '1.20'
library(energy)
packageVersion("energy")
## [1] '1.7.5'
library(broom)
packageVersion("broom")
## [1] '0.5.0'
library(plyr)
packageVersion("plyr")
## [1] '1.8.4'
library(kableExtra)
packageVersion("kableExtra")
## [1] '0.9.0'
library(foreach)
packageVersion("foreach")
## [1] '1.4.4'
library(doParallel)
## Loading required package: iterators
## Loading required package: parallel
packageVersion("doParallel")
## [1] '1.0.14'
set.seed(0)
GSEA was separately run and the enrichment results are saved. We upload the results and select the significant findings.
gsea_results <- read.csv("./GSEA diabetes/gsea_diabetes_enrichment_results_v6.2.csv", sep = ",", row.names = 1)
# rownames(gsea_results) <- (rownames(gsea_results)) #tolower removed
gsea_results_significant <- subset(gsea_results, NOM.p.val <0.05 )
We use the colapsed symbols to genes expression data for expressions. GSEA uses a chip functoin for connecting the uncollapsed to collapsed data. I am currently figuring out how ti perfprms that step. For now not collapsing serves the purpose. Genotypes are 33 mutants and 17 wild types. Pathways are read as done is GSEA. To remain consistent with GSEA we remove the pathways with sizes below 15 and above 500 as well as pathways that have less than 15 genes present in inside the expression matrix.
expressions <- read.csv("./GSEA diabetes/Diabetes_collapsed_symbols_R.csv", sep = ",", row.names = 1)
genotypes <- read.csv("./GSEA diabetes/Diabetes_genotype.txt", sep=" ", header = F)
genotypes <- as.vector(unname(ifelse( genotypes==1,1,0)))
gene_names <- rownames(expressions)
expressions <- expressions[-1]
expressions <- t(expressions)
dim(expressions)
## [1] 34 15056
pathway <- read.csv("./msigdb_v6.2_files_to_download_locally/msigdb_v6.2_GMTs_R/curated gene sets/c2.all.v6.2.symbols.csv", sep = ",", row.names = 1,na.strings = "", colClasses="character")
pathway <- pathway[,-1]
pathway <- t(pathway)
row.names(pathway) <- NULL
pathway <- as.data.frame(pathway)
pathway=lapply(pathway, function(x) x[!is.na(x)] )
pathway=lapply(pathway, function(x) as.character(x))
# pathway_collapsed <- pathway[sapply(pathway,function(x) {(15 <= length(x)) &&(length(x) <= 500)&& sum(colnames(expressions)%in%x)>15})]
pathway_collapsed <- pathway[names(pathway) %in% rownames(gsea_results)]
min(sapply(pathway_collapsed,length))
## [1] 15
individual_pathway_length <- sapply(pathway_collapsed,length)
gene_number <- length(gene_names)
pathway_number <- length(individual_pathway_length)
pathway_number
## [1] 3525
Expressions concordant with specific pathways are chosen and dcor and univariate t.test are applied on them. The univariate test is adjusted for FDR correction.
dcor_results <- list()
univariate_results <- list()
univariate_results_adjusted <- list()
for (ii in 1:length(pathway_collapsed)){
pathway_expressions <- expressions[,colnames(expressions)%in% pathway_collapsed[[ii]]]
dcor_results[ii] <- dcor((pathway_expressions),(genotypes))
}
names(dcor_results) <- names( pathway_collapsed)
set.seed(0)
# surrogate_dcor <- list()
num_simulation <- 999
cl<-makeCluster(6)
registerDoParallel(cl)
surrogate_dcor <- foreach (ii = 1:pathway_number, .export = c("num_simulation","gene_number","individual_pathway_length","genotypes"), .packages = "energy") %dopar%{
if(ii%%100==0) print(ii)
aux_dcor <- NULL
for ( jj in 1: num_simulation)
{
aux_genes <- sample(1:gene_number,individual_pathway_length[ii])
aux_dcor[jj] <- dcor(expressions[,aux_genes],genotypes)
}
# surrogate_dcor[[ii]] <- aux_dcor
aux_dcor
}
## Warning in e$fun(obj, substitute(ex), parent.frame(), e$data):
## already exporting variable(s): num_simulation, gene_number,
## individual_pathway_length, genotypes
stopCluster(cl)
nominal_dcor_pvalues <- sapply(1:pathway_number, function(x) (1+(sum(surrogate_dcor[[x]]>dcor_results[x])))/(1+num_simulation))
names(nominal_dcor_pvalues) <- names( pathway_collapsed)
head(sort(nominal_dcor_pvalues),10)
## KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP
## 0.001
## HEIDENBLAD_AMPLICON_12P11_12_UP
## 0.001
## LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_LARGE_VS_TINY_UP
## 0.001
## GROSS_HYPOXIA_VIA_HIF1A_UP
## 0.001
## MORI_SMALL_PRE_BII_LYMPHOCYTE_UP
## 0.001
## SHEPARD_CRUSH_AND_BURN_MUTANT_UP
## 0.001
## MA_MYELOID_DIFFERENTIATION_DN
## 0.001
## ZHENG_FOXP3_TARGETS_IN_THYMUS_UP
## 0.001
## LEE_DIFFERENTIATING_T_LYMPHOCYTE
## 0.001
## WHITFIELD_CELL_CYCLE_G2
## 0.001
dcor_significant_pathways_p.value <- sort(nominal_dcor_pvalues[nominal_dcor_pvalues <0.05])
nominal_dcor_q_values <- p.adjust(nominal_dcor_pvalues , method = "fdr")
# nominal_dcor_q_values
nominal_dcor_q_values_under_25 <- sort(nominal_dcor_q_values[nominal_dcor_q_values<0.25])
nominal_dcor_q_values_under_25
## named numeric(0)
Mutually_identified_in_GSEA_dcor <- intersect(names(dcor_significant_pathways_p.value), rownames(gsea_results_significant))
Mutually_identified_in_GSEA_dcor
## [1] "LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_LARGE_VS_TINY_UP"
## [2] "GROSS_HYPOXIA_VIA_HIF1A_UP"
## [3] "REACTOME_MEIOSIS"
## [4] "REACTOME_CHROMOSOME_MAINTENANCE"
## [5] "REACTOME_MEIOTIC_SYNAPSIS"
## [6] "MORI_IMMATURE_B_LYMPHOCYTE_UP"
## [7] "REACTOME_MRNA_CAPPING"
## [8] "LANDIS_ERBB2_BREAST_TUMORS_65_UP"
## [9] "FERRANDO_TAL1_NEIGHBORS"
## [10] "REACTOME_TRANSCRIPTION_COUPLED_NER_TC_NER"
## [11] "SMID_BREAST_CANCER_ERBB2_UP"
## [12] "REACTOME_NUCLEOTIDE_EXCISION_REPAIR"
## [13] "OHGUCHI_LIVER_HNF4A_TARGETS_UP"
## [14] "GAUSSMANN_MLL_AF4_FUSION_TARGETS_B_UP"
## [15] "KEGG_HUNTINGTONS_DISEASE"
## [16] "PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP"
## [17] "SATO_SILENCED_EPIGENETICALLY_IN_PANCREATIC_CANCER"
## [18] "WONG_MITOCHONDRIA_GENE_MODULE"
## [19] "KEGG_OXIDATIVE_PHOSPHORYLATION"
## [20] "FAELT_B_CLL_WITH_VH_REARRANGEMENTS_DN"
## [21] "REACTOME_DNA_REPAIR"
## [22] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13"
## [23] "BIDUS_METASTASIS_DN"
## [24] "MOOTHA_VOXPHOS"
Significant_in_dcor_not_in_GSEA <- setdiff(names(dcor_significant_pathways_p.value),Mutually_identified_in_GSEA_dcor)
pvalue_of_disparities <- rbind(dcor_significant_pathways_p.value[Significant_in_dcor_not_in_GSEA],gsea_results[Significant_in_dcor_not_in_GSEA,]$NOM.p.val)
rownames(pvalue_of_disparities) <- c("MPEA","GSEA")
pvalue_of_disparities%>%
kable("html", digits = 4, longtable = TRUE) %>%
kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
row_spec(0, angle = -0)
| KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP | HEIDENBLAD_AMPLICON_12P11_12_UP | MORI_SMALL_PRE_BII_LYMPHOCYTE_UP | SHEPARD_CRUSH_AND_BURN_MUTANT_UP | MA_MYELOID_DIFFERENTIATION_DN | ZHENG_FOXP3_TARGETS_IN_THYMUS_UP | LEE_DIFFERENTIATING_T_LYMPHOCYTE | WHITFIELD_CELL_CYCLE_G2 | CEBALLOS_TARGETS_OF_TP53_AND_MYC_UP | BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN | DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER | SMITH_TERT_TARGETS_DN | WANG_TARGETS_OF_MLL_CBP_FUSION_DN | ZHANG_TLX_TARGETS_60HR_DN | WIERENGA_STAT5A_TARGETS_UP | ENK_UV_RESPONSE_KERATINOCYTE_DN | FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN | FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP | FRIDMAN_IMMORTALIZATION_DN | GEORGES_TARGETS_OF_MIR192_AND_MIR215 | FOSTER_TOLERANT_MACROPHAGE_UP | WALLACE_PROSTATE_CANCER_RACE_UP | WATANABE_ULCERATIVE_COLITIS_WITH_CANCER_UP | WIERENGA_STAT5A_TARGETS_GROUP1 | BHAT_ESR1_TARGETS_VIA_AKT1_UP | FISCHER_DIRECT_P53_TARGETS_META_ANALYSIS | PID_PTP1B_PATHWAY | SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_UP | MITSIADES_RESPONSE_TO_APLIDIN_UP | PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7 | OISHI_CHOLANGIOMA_STEM_CELL_LIKE_DN | GARY_CD5_TARGETS_DN | CAFFAREL_RESPONSE_TO_THC_DN | OUILLETTE_CLL_13Q14_DELETION_DN | ENGELMANN_CANCER_PROGENITORS_DN | REACTOME_ABORTIVE_ELONGATION_OF_HIV1_TRANSCRIPT_IN_THE_ABSENCE_OF_TAT | HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_DN | IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_UP | BHAT_ESR1_TARGETS_NOT_VIA_AKT1_UP | KEGG_STEROID_BIOSYNTHESIS | KEGG_RNA_POLYMERASE | PID_EPHA_FWDPATHWAY | JAEGER_METASTASIS_DN | LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP | WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_DN | BIOCARTA_CARDIACEGF_PATHWAY | REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PI3KGAMMA | FORTSCHEGGER_PHF8_TARGETS_UP | LIU_PROSTATE_CANCER_UP | LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q | BROWNE_HCMV_INFECTION_48HR_UP | HORTON_SREBF_TARGETS | BIOCARTA_PAR1_PATHWAY | REACTOME_MICRORNA_MIRNA_BIOGENESIS | REACTOME_PI3K_AKT_ACTIVATION | REACTOME_FORMATION_OF_THE_HIV1_EARLY_ELONGATION_COMPLEX | BORCZUK_MALIGNANT_MESOTHELIOMA_UP | REACTOME_FORMATION_OF_TRANSCRIPTION_COUPLED_NER_TC_NER_REPAIR_COMPLEX | NAGASHIMA_NRG1_SIGNALING_DN | CHEBOTAEV_GR_TARGETS_DN | GEISS_RESPONSE_TO_DSRNA_DN | LABBE_WNT3A_TARGETS_DN | HELLEBREKERS_SILENCED_DURING_TUMOR_ANGIOGENESIS | KEGG_PYRIMIDINE_METABOLISM | FARMER_BREAST_CANCER_APOCRINE_VS_LUMINAL | MACLACHLAN_BRCA1_TARGETS_UP | QI_HYPOXIA_TARGETS_OF_HIF1A_AND_FOXA2 | PID_S1P_S1P2_PATHWAY | YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_5 | PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP | DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_DN | PID_LIS1_PATHWAY | REACTOME_REGULATORY_RNA_PATHWAYS | REACTOME_RNA_POL_II_TRANSCRIPTION_PRE_INITIATION_AND_PROMOTER_OPENING | REACTOME_GPVI_MEDIATED_ACTIVATION_CASCADE | SHI_SPARC_TARGETS_UP | ZHANG_ANTIVIRAL_RESPONSE_TO_RIBAVIRIN_DN | TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_UP | PLASARI_NFIC_TARGETS_BASAL_UP | PID_PRL_SIGNALING_EVENTS_PATHWAY | PID_S1P_S1P3_PATHWAY | PID_EPHA2_FWD_PATHWAY | HOUSTIS_ROS | ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_DN | PID_AVB3_INTEGRIN_PATHWAY | DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP | SANSOM_APC_TARGETS_DN | RAMPON_ENRICHED_LEARNING_ENVIRONMENT_LATE_UP | PID_ECADHERIN_KERATINOCYTE_PATHWAY | REACTOME_G_PROTEIN_BETA_GAMMA_SIGNALLING | PETROVA_PROX1_TARGETS_UP | BROWNE_HCMV_INFECTION_6HR_DN | CHEN_ETV5_TARGETS_TESTIS | NADLER_HYPERGLYCEMIA_AT_OBESITY | DAZARD_RESPONSE_TO_UV_NHEK_DN | WINNEPENNINCKX_MELANOMA_METASTASIS_DN | BIOCARTA_CDC42RAC_PATHWAY | PID_P53_REGULATION_PATHWAY | GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREY_DN | MULLIGHAN_NPM1_SIGNATURE_3_UP | SHEN_SMARCA2_TARGETS_UP | SA_TRKA_RECEPTOR | PID_TGFBR_PATHWAY | REACTOME_SEMA4D_IN_SEMAPHORIN_SIGNALING | PETRETTO_CARDIAC_HYPERTROPHY | ONDER_CDH1_TARGETS_1_UP | BILD_MYC_ONCOGENIC_SIGNATURE | RIGGI_EWING_SARCOMA_PROGENITOR_DN | PID_WNT_NONCANONICAL_PATHWAY | GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_DN | VERHAAK_GLIOBLASTOMA_NEURAL | KASLER_HDAC7_TARGETS_1_DN | PID_S1P_S1P1_PATHWAY | TARTE_PLASMA_CELL_VS_PLASMABLAST_DN | MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_DN | PLASARI_TGFB1_TARGETS_10HR_DN | REACTOME_RNA_POL_III_TRANSCRIPTION_TERMINATION | MENSE_HYPOXIA_UP | BOCHKIS_FOXA2_TARGETS | BIOCARTA_RAS_PATHWAY | PID_SYNDECAN_4_PATHWAY | REACTOME_RNA_POL_III_TRANSCRIPTION | MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP | MULLIGHAN_NPM1_MUTATED_SIGNATURE_2_UP | BERTUCCI_INVASIVE_CARCINOMA_DUCTAL_VS_LOBULAR_DN | GAJATE_RESPONSE_TO_TRABECTEDIN_UP | MARIADASON_RESPONSE_TO_CURCUMIN_SULINDAC_5 | COATES_MACROPHAGE_M1_VS_M2_DN | LIN_NPAS4_TARGETS_UP | REACTOME_G_ALPHA1213_SIGNALLING_EVENTS | FARMER_BREAST_CANCER_APOCRINE_VS_BASAL | JOHNSTONE_PARVB_TARGETS_3_UP | KENNY_CTNNB1_TARGETS_DN | BRACHAT_RESPONSE_TO_CAMPTOTHECIN_UP | WANG_SMARCE1_TARGETS_UP | LEIN_CHOROID_PLEXUS_MARKERS | BERNARD_PPAPDC1B_TARGETS_UP | BROWNE_HCMV_INFECTION_4HR_DN | MCBRYAN_PUBERTAL_TGFB1_TARGETS_DN | HU_ANGIOGENESIS_DN | SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY | NUYTTEN_NIPP1_TARGETS_UP | SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP | MURAKAMI_UV_RESPONSE_6HR_DN | BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN | BYSTRYKH_HEMATOPOIESIS_STEM_CELL_SCP2_QTL_TRANS | WIERENGA_STAT5A_TARGETS_GROUP2 | CASORELLI_APL_SECONDARY_VS_DE_NOVO_UP | BASAKI_YBX1_TARGETS_UP | RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP | MARTORIATI_MDM4_TARGETS_FETAL_LIVER_UP | LENAOUR_DENDRITIC_CELL_MATURATION_DN | WINZEN_DEGRADED_VIA_KHSRP | LIU_SOX4_TARGETS_UP | PENG_RAPAMYCIN_RESPONSE_UP | ACOSTA_PROLIFERATION_INDEPENDENT_MYC_TARGETS_UP | BIOCARTA_EDG1_PATHWAY | PID_ECADHERIN_NASCENT_AJ_PATHWAY | NOJIMA_SFRP2_TARGETS_UP | ODONNELL_METASTASIS_DN | LEE_TARGETS_OF_PTCH1_AND_SUFU_DN | UEDA_PERIFERAL_CLOCK | HASLINGER_B_CLL_WITH_MUTATED_VH_GENES | MCCLUNG_COCAINE_REWARD_5D | CADWELL_ATG16L1_TARGETS_DN | MIKKELSEN_ES_HCP_WITH_H3_UNMETHYLATED | LI_INDUCED_T_TO_NATURAL_KILLER_DN | GUILLAUMOND_KLF10_TARGETS_DN | BIOCARTA_PTDINS_PATHWAY | SAMOLS_TARGETS_OF_KHSV_MIRNAS_DN | MARKS_HDAC_TARGETS_UP | VANTVEER_BREAST_CANCER_ESR1_UP | GUTIERREZ_MULTIPLE_MYELOMA_UP | REACTOME_SEMA4D_INDUCED_CELL_MIGRATION_AND_GROWTH_CONE_COLLAPSE | REACTOME_CHOLESTEROL_BIOSYNTHESIS | ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP | RODWELL_AGING_KIDNEY_NO_BLOOD_DN | AMIT_EGF_RESPONSE_40_MCF10A | SCHLINGEMANN_SKIN_CARCINOGENESIS_TPA_UP | REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_2_PROMOTER | MOREIRA_RESPONSE_TO_TSA_UP | MURAKAMI_UV_RESPONSE_24HR | YAMASHITA_METHYLATED_IN_PROSTATE_CANCER | FONTAINE_THYROID_TUMOR_UNCERTAIN_MALIGNANCY_UP | GOLUB_ALL_VS_AML_DN | MASSARWEH_RESPONSE_TO_ESTRADIOL | BRUECKNER_TARGETS_OF_MIRLET7A3_UP | REACTOME_PEROXISOMAL_LIPID_METABOLISM | REACTOME_MRNA_SPLICING_MINOR_PATHWAY | VARELA_ZMPSTE24_TARGETS_UP | DE_YY1_TARGETS_UP | TIAN_TNF_SIGNALING_NOT_VIA_NFKB | HUANG_GATA2_TARGETS_UP | KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT | REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_3_PROMOTER | GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_UP | PUJANA_BRCA2_PCC_NETWORK | RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_DN | CUI_GLUCOSE_DEPRIVATION | BIOCARTA_RACCYCD_PATHWAY | GRAHAM_CML_DIVIDING_VS_NORMAL_QUIESCENT_DN | KEEN_RESPONSE_TO_ROSIGLITAZONE_UP | BURTON_ADIPOGENESIS_6 | COATES_MACROPHAGE_M1_VS_M2_UP | MANALO_HYPOXIA_DN | VERRECCHIA_EARLY_RESPONSE_TO_TGFB1 | SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_1 | AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_DN | REACTOME_P75_NTR_RECEPTOR_MEDIATED_SIGNALLING | MISSIAGLIA_REGULATED_BY_METHYLATION_UP | SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_DN | JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_UP | SCHMIDT_POR_TARGETS_IN_LIMB_BUD_UP | BIOCARTA_P53HYPOXIA_PATHWAY | PID_IL4_2PATHWAY | YAGI_AML_RELAPSE_PROGNOSIS | HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_DN | YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_1 | ODONNELL_TARGETS_OF_MYC_AND_TFRC_UP | RICKMAN_METASTASIS_UP | CUI_TCF21_TARGETS_DN | YAGI_AML_WITH_T_8_21_TRANSLOCATION | WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_UP | TERAMOTO_OPN_TARGETS_CLUSTER_7 | PETRETTO_HEART_MASS_QTL_CIS_DN | LAMB_CCND1_TARGETS | GENTILE_UV_LOW_DOSE_UP | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MPEA | 0.0010 | 0.0010 | 0.0010 | 0.0010 | 0.0010 | 0.0010 | 0.0010 | 0.0010 | 0.0020 | 0.002 | 0.0020 | 0.0020 | 0.0020 | 0.0020 | 0.0020 | 0.0030 | 0.0030 | 0.0040 | 0.0040 | 0.0040 | 0.0040 | 0.0040 | 0.0050 | 0.005 | 0.005 | 0.0050 | 0.0060 | 0.0060 | 0.0060 | 0.006 | 0.0060 | 0.0070 | 0.0070 | 0.0070 | 0.0070 | 0.008 | 0.0080 | 0.0080 | 0.0080 | 0.0090 | 0.0090 | 0.009 | 0.0090 | 0.0090 | 0.0090 | 0.0100 | 0.0100 | 0.0100 | 0.0110 | 0.0110 | 0.0110 | 0.0110 | 0.0120 | 0.0120 | 0.012 | 0.0120 | 0.0120 | 0.0130 | 0.0130 | 0.0130 | 0.0130 | 0.0130 | 0.0130 | 0.0140 | 0.014 | 0.0140 | 0.0140 | 0.0150 | 0.0150 | 0.0160 | 0.0160 | 0.017 | 0.0170 | 0.0170 | 0.0170 | 0.0170 | 0.0170 | 0.017 | 0.0170 | 0.018 | 0.0180 | 0.018 | 0.0180 | 0.0180 | 0.019 | 0.0190 | 0.0190 | 0.0190 | 0.0200 | 0.0200 | 0.0200 | 0.0200 | 0.0200 | 0.0210 | 0.0210 | 0.0210 | 0.0220 | 0.0220 | 0.0220 | 0.0220 | 0.0220 | 0.023 | 0.023 | 0.0230 | 0.023 | 0.0230 | 0.0230 | 0.023 | 0.0240 | 0.0240 | 0.0240 | 0.0240 | 0.0250 | 0.0250 | 0.0250 | 0.0250 | 0.0260 | 0.0260 | 0.0260 | 0.0280 | 0.0280 | 0.0280 | 0.0280 | 0.0280 | 0.0280 | 0.0280 | 0.0280 | 0.0280 | 0.0280 | 0.0290 | 0.0290 | 0.0290 | 0.0300 | 0.0300 | 0.0300 | 0.0300 | 0.0300 | 0.0300 | 0.0310 | 0.0310 | 0.0310 | 0.031 | 0.0310 | 0.0310 | 0.0310 | 0.031 | 0.0310 | 0.0320 | 0.0320 | 0.032 | 0.0320 | 0.0320 | 0.0320 | 0.0330 | 0.0330 | 0.033 | 0.0340 | 0.0340 | 0.0340 | 0.0340 | 0.0340 | 0.0340 | 0.0340 | 0.0340 | 0.0340 | 0.0340 | 0.0340 | 0.034 | 0.0350 | 0.0350 | 0.0350 | 0.0350 | 0.0350 | 0.0360 | 0.0360 | 0.0360 | 0.0360 | 0.0370 | 0.0370 | 0.0380 | 0.0380 | 0.0380 | 0.0380 | 0.0380 | 0.0390 | 0.0390 | 0.0390 | 0.040 | 0.0400 | 0.0400 | 0.0400 | 0.0400 | 0.0400 | 0.041 | 0.0410 | 0.0410 | 0.0410 | 0.0410 | 0.0410 | 0.042 | 0.042 | 0.0420 | 0.0420 | 0.0420 | 0.0430 | 0.0430 | 0.0430 | 0.0430 | 0.044 | 0.045 | 0.0450 | 0.0450 | 0.0450 | 0.0470 | 0.0470 | 0.0470 | 0.0470 | 0.0470 | 0.048 | 0.0480 | 0.0480 | 0.0480 | 0.0490 | 0.0490 | 0.0490 | 0.0490 | 0.0490 |
| GSEA | 0.7939 | 0.5246 | 0.5202 | 0.1169 | 0.2189 | 0.8133 | 0.7427 | 0.9876 | 0.2354 | 0.632 | 0.4907 | 0.3854 | 0.7294 | 0.1515 | 0.2618 | 0.6447 | 0.7864 | 0.1394 | 0.7462 | 0.2096 | 0.3752 | 0.7976 | 0.2458 | 0.247 | 0.741 | 0.6335 | 0.9792 | 0.2016 | 0.0977 | 0.497 | 0.5279 | 0.3593 | 0.7019 | 0.1467 | 0.7563 | 0.373 | 0.5545 | 0.9084 | 0.8959 | 0.1972 | 0.3138 | 0.302 | 0.8517 | 0.2785 | 0.1566 | 0.4626 | 0.2172 | 0.6378 | 0.1481 | 0.0638 | 0.4706 | 0.6083 | 0.2609 | 0.4038 | 0.917 | 0.1454 | 0.8423 | 0.0541 | 0.1127 | 0.2548 | 0.0813 | 0.4839 | 0.9648 | 0.3037 | 0.703 | 0.5885 | 0.6437 | 0.2688 | 0.3533 | 0.7234 | 0.7505 | 0.384 | 0.4038 | 0.0671 | 0.6747 | 0.9248 | 0.4812 | 0.175 | 0.4008 | 0.256 | 0.9014 | 0.211 | 0.2281 | 0.6826 | 0.996 | 0.8059 | 0.8822 | 0.4369 | 0.3123 | 0.1959 | 0.7256 | 0.0855 | 0.5264 | 0.7196 | 0.5838 | 0.7666 | 0.7375 | 0.3551 | 0.4255 | 0.3267 | 0.8546 | 0.854 | 0.782 | 0.9123 | 0.880 | 0.7146 | 0.8869 | 1.000 | 0.4346 | 0.1713 | 0.3777 | 0.7206 | 0.3119 | 0.6093 | 0.2385 | 0.9283 | 0.0601 | 0.2758 | 0.2924 | 0.9403 | 0.5322 | 0.7442 | 0.5078 | 0.8377 | 0.6223 | 0.3733 | 0.7515 | 0.6968 | 0.5515 | 0.0881 | 0.9593 | 0.8516 | 0.4942 | 0.4124 | 0.5445 | 0.9053 | 0.6982 | 0.6963 | 0.6245 | 0.0678 | 0.1904 | 0.089 | 0.2358 | 0.7084 | 0.7202 | 0.666 | 0.6593 | 0.9772 | 0.4047 | 0.876 | 0.3984 | 0.7992 | 0.6371 | 0.4286 | 0.7784 | 0.384 | 0.8806 | 0.3631 | 0.2772 | 0.4688 | 0.2615 | 0.9724 | 0.0972 | 0.8103 | 0.6754 | 0.6888 | 0.2965 | 0.368 | 0.8613 | 0.4838 | 0.7025 | 0.7947 | 0.8244 | 0.6598 | 0.5293 | 0.2464 | 0.0569 | 0.0754 | 0.5215 | 0.5219 | 0.6068 | 0.3401 | 0.5592 | 0.4038 | 0.2063 | 0.2093 | 0.6701 | 0.292 | 0.1794 | 0.9941 | 0.1357 | 0.2604 | 0.4879 | 0.246 | 0.7146 | 0.4928 | 0.8337 | 0.8665 | 0.2231 | 0.625 | 0.383 | 0.7918 | 0.1412 | 0.4199 | 0.5386 | 0.4118 | 0.3041 | 0.5193 | 0.623 | 0.657 | 0.1187 | 0.1116 | 0.4714 | 0.0547 | 0.8487 | 0.7898 | 0.6578 | 0.5984 | 0.349 | 0.4052 | 0.6274 | 0.8939 | 0.3212 | 0.5247 | 0.1475 | 0.8735 | 0.5937 |
Significant_in_GSEA_not_in_dcor <- setdiff(rownames(gsea_results_significant),Mutually_identified_in_GSEA_dcor)
pvalue_of_disparities <- rbind(nominal_dcor_pvalues[Significant_in_GSEA_not_in_dcor],gsea_results[Significant_in_GSEA_not_in_dcor,]$NOM.p.val)
rownames(pvalue_of_disparities) <- c("MPEA","GSEA")
pvalue_of_disparities %>%
kable("html", digits = 4, longtable = TRUE) %>%
kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
row_spec(0, angle = -0)
| LUI_TARGETS_OF_PAX8_PPARG_FUSION | LUI_THYROID_CANCER_CLUSTER_3 | ANDERSEN_LIVER_CANCER_KRT19_UP | REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_ | POMEROY_MEDULLOBLASTOMA_PROGNOSIS_DN | MCBRYAN_PUBERTAL_BREAST_3_4WK_DN | REACTOME_INFLUENZA_LIFE_CYCLE | LANDIS_ERBB2_BREAST_TUMORS_324_UP | KEGG_ALZHEIMERS_DISEASE | REACTOME_METABOLISM_OF_RNA | CHNG_MULTIPLE_MYELOMA_HYPERPLOID_UP | REACTOME_RESPIRATORY_ELECTRON_TRANSPORT | FAELT_B_CLL_WITH_VH_REARRANGEMENTS_UP | REACTOME_DOWNREGULATION_OF_SMAD2_3_SMAD4_TRANSCRIPTIONAL_ACTIVITY | REACTOME_METABOLISM_OF_MRNA | PECE_MAMMARY_STEM_CELL_UP | KEGG_NUCLEOTIDE_EXCISION_REPAIR | TONG_INTERACT_WITH_PTTG1 | EHLERS_ANEUPLOIDY_UP | YAMASHITA_LIVER_CANCER_WITH_EPCAM_UP | KANNAN_TP53_TARGETS_DN | DUNNE_TARGETS_OF_AML1_MTG8_FUSION_DN | MEINHOLD_OVARIAN_CANCER_LOW_GRADE_DN | REACTOME_NONSENSE_MEDIATED_DECAY_ENHANCED_BY_THE_EXON_JUNCTION_COMPLEX | REACTOME_TRANSLATION | REACTOME_SYNTHESIS_AND_INTERCONVERSION_OF_NUCLEOTIDE_DI_AND_TRIPHOSPHATES | TAKAO_RESPONSE_TO_UVB_RADIATION_UP | BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_DN | REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE | HUMMERICH_BENIGN_SKIN_TUMOR_UP | HSIAO_HOUSEKEEPING_GENES | JAZAG_TGFB1_SIGNALING_UP | BAE_BRCA1_TARGETS_UP | KEGG_RIBOSOME | NUTT_GBM_VS_AO_GLIOMA_DN | MARTINEZ_RESPONSE_TO_TRABECTEDIN_UP | KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_DN | REACTOME_METABOLISM_OF_PROTEINS | BILANGES_SERUM_RESPONSE_TRANSLATION | LANDIS_BREAST_CANCER_PROGRESSION_UP | NAKAYAMA_FGF2_TARGETS | HUNSBERGER_EXERCISE_REGULATED_GENES | LUI_THYROID_CANCER_PAX8_PPARG_DN | WENG_POR_TARGETS_GLOBAL_UP | REACTOME_PEPTIDE_CHAIN_ELONGATION | NIKOLSKY_BREAST_CANCER_8P12_P11_AMPLICON | IRITANI_MAD1_TARGETS_DN | YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_17 | LEE_LIVER_CANCER_SURVIVAL_DN | REACTOME_SIGNAL_AMPLIFICATION | WANG_RESPONSE_TO_FORSKOLIN_UP | JIANG_AGING_HYPOTHALAMUS_UP | PARK_HSC_VS_MULTIPOTENT_PROGENITORS_DN | HOLLEMAN_ASPARAGINASE_RESISTANCE_ALL_UP | KEGG_BASAL_TRANSCRIPTION_FACTORS | OSMAN_BLADDER_CANCER_DN | YANG_BREAST_CANCER_ESR1_UP | ZHAN_MULTIPLE_MYELOMA_HP_UP | PARK_HSC_MARKERS | REACTOME_TGF_BETA_RECEPTOR_SIGNALING_ACTIVATES_SMADS | WANG_TUMOR_INVASIVENESS_UP | REACTOME_GLOBAL_GENOMIC_NER_GG_NER | GEORGES_CELL_CYCLE_MIR192_TARGETS | MAINA_VHL_TARGETS_DN | CHEN_PDGF_TARGETS | SCHRAMM_INHBA_TARGETS_DN | FAELT_B_CLL_WITH_VH3_21_DN | BOUDOUKHA_BOUND_BY_IGF2BP2 | NATSUME_RESPONSE_TO_INTERFERON_BETA_DN | REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE | GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN | MURAKAMI_UV_RESPONSE_1HR_UP | PID_PI3K_PLC_TRK_PATHWAY | REACTOME_ADP_SIGNALLING_THROUGH_P2RY1 | WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP | CHANGOLKAR_H2AFY_TARGETS_UP | BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_UP | PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_DN | BORLAK_LIVER_CANCER_EGF_UP | REACTOME_G_ALPHA_Z_SIGNALLING_EVENTS | YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9 | KIM_MYC_AMPLIFICATION_TARGETS_UP | LINDGREN_BLADDER_CANCER_CLUSTER_1_UP | CHANGOLKAR_H2AFY_TARGETS_DN | HORIUCHI_WTAP_TARGETS_DN | SASAKI_ADULT_T_CELL_LEUKEMIA | GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN | REACTOME_INTEGRATION_OF_ENERGY_METABOLISM | DELASERNA_MYOD_TARGETS_UP | KASLER_HDAC7_TARGETS_2_DN | PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_DN | SHIN_B_CELL_LYMPHOMA_CLUSTER_8 | DOANE_BREAST_CANCER_ESR1_DN | BIOCARTA_AGR_PATHWAY | REACTOME_RNA_POL_I_PROMOTER_OPENING | REACTOME_HDL_MEDIATED_LIPID_TRANSPORT | FAELT_B_CLL_WITH_VH3_21_UP | KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3 | HASLINGER_B_CLL_WITH_6Q21_DELETION | KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_DN | KEGG_PPAR_SIGNALING_PATHWAY | REACTOME_DEPOSITION_OF_NEW_CENPA_CONTAINING_NUCLEOSOMES_AT_THE_CENTROMERE | MIKKELSEN_MEF_LCP_WITH_H3K27ME3 | XU_GH1_EXOGENOUS_TARGETS_DN | ABE_VEGFA_TARGETS_2HR | FIGUEROA_AML_METHYLATION_CLUSTER_1_DN | REACTOME_LIPOPROTEIN_METABOLISM | BONOME_OVARIAN_CANCER_POOR_SURVIVAL_DN | BIOCARTA_UCALPAIN_PATHWAY | ST_T_CELL_SIGNAL_TRANSDUCTION | DING_LUNG_CANCER_MUTATED_SIGNIFICANTLY | HUMMERICH_MALIGNANT_SKIN_TUMOR_DN | CHEMELLO_SOLEUS_VS_EDL_MYOFIBERS_UP | PID_NCADHERIN_PATHWAY | HUMMERICH_BENIGN_SKIN_TUMOR_DN | REACTOME_PACKAGING_OF_TELOMERE_ENDS | LEI_HOXC8_TARGETS_DN | PID_BARD1_PATHWAY | FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_UP | BIOCARTA_MAL_PATHWAY | XU_AKT1_TARGETS_6HR | PID_INSULIN_GLUCOSE_PATHWAY | REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS | SA_B_CELL_RECEPTOR_COMPLEXES | SCHEIDEREIT_IKK_INTERACTING_PROTEINS | REACTOME_BILE_ACID_AND_BILE_SALT_METABOLISM | ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_DN | BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_UP | RIZ_ERYTHROID_DIFFERENTIATION_HEMGN | MEISSNER_BRAIN_HCP_WITH_H3K27ME3 | REACTOME_SEMAPHORIN_INTERACTIONS | KUMAR_AUTOPHAGY_NETWORK | SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_DN | KENNY_CTNNB1_TARGETS_UP | OXFORD_RALA_OR_RALB_TARGETS_UP | LABBE_TARGETS_OF_TGFB1_AND_WNT3A_UP | MIKKELSEN_NPC_HCP_WITH_H3K27ME3 | BIOCARTA_HER2_PATHWAY | FIGUEROA_AML_METHYLATION_CLUSTER_3_DN | KYNG_DNA_DAMAGE_BY_4NQO | MULLIGHAN_NPM1_SIGNATURE_3_DN | PID_IL23_PATHWAY | REACTOME_MEIOTIC_RECOMBINATION | MIKKELSEN_MCV6_HCP_WITH_H3K27ME3 | CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP | QI_HYPOXIA | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MPEA | 0.325 | 0.283 | 0.713 | 0.0520 | 0.419 | 0.2990 | 0.6250 | 0.118 | 0.0780 | 0.6150 | 0.5100 | 0.0730 | 0.3400 | 0.212 | 0.6370 | 0.6340 | 0.1550 | 0.7290 | 0.4960 | 0.7090 | 0.6040 | 0.4850 | 0.165 | 0.6160 | 0.6400 | 0.8390 | 0.169 | 0.1780 | 0.6730 | 0.1910 | 0.6410 | 0.278 | 0.1020 | 0.6720 | 0.4620 | 0.2720 | 0.5370 | 0.4930 | 0.4820 | 0.8820 | 0.0670 | 0.8660 | 0.3520 | 0.6730 | 0.6540 | 0.4560 | 0.1790 | 0.1190 | 0.5050 | 0.4040 | 0.2130 | 0.7620 | 0.1650 | 0.3790 | 0.253 | 0.524 | 0.7410 | 0.5050 | 0.6830 | 0.1370 | 0.4240 | 0.1030 | 0.2840 | 0.1630 | 0.091 | 0.1440 | 0.0830 | 0.3890 | 0.7050 | 0.144 | 0.0850 | 0.1600 | 0.8210 | 0.4650 | 0.6490 | 0.2340 | 0.0910 | 0.4060 | 0.2480 | 0.5060 | 0.4600 | 0.1790 | 0.3670 | 0.936 | 0.1680 | 0.1920 | 0.6280 | 0.2920 | 0.933 | 0.3640 | 0.783 | 0.655 | 0.611 | 0.9790 | 0.5370 | 0.062 | 0.625 | 0.329 | 0.954 | 0.9900 | 0.231 | 0.9180 | 0.9930 | 0.5700 | 0.581 | 0.4930 | 0.1740 | 0.7820 | 0.9600 | 0.0960 | 0.6210 | 0.8220 | 0.939 | 0.9820 | 0.8330 | 0.9690 | 0.5840 | 0.6320 | 0.9130 | 0.9690 | 0.949 | 0.191 | 0.5150 | 0.6070 | 0.9460 | 0.5350 | 0.8790 | 0.5360 | 0.9220 | 0.4710 | 0.1050 | 0.8080 | 0.6470 | 0.0770 | 0.3900 | 0.9130 | 0.2370 | 0.1440 | 0.5360 | 0.0700 | 0.8150 | 0.1750 | 0.4160 | 0.2910 | 0.2450 | 0.6140 |
| GSEA | 0.002 | 0.004 | 0.004 | 0.0177 | 0.002 | 0.0019 | 0.0158 | 0.000 | 0.0121 | 0.0198 | 0.0199 | 0.0141 | 0.0061 | 0.010 | 0.0355 | 0.0326 | 0.0115 | 0.0219 | 0.0161 | 0.0256 | 0.0124 | 0.0166 | 0.002 | 0.0321 | 0.0325 | 0.0059 | 0.014 | 0.0082 | 0.0383 | 0.0123 | 0.0238 | 0.000 | 0.0219 | 0.0378 | 0.0339 | 0.0125 | 0.0208 | 0.0374 | 0.0429 | 0.0281 | 0.0337 | 0.0185 | 0.0243 | 0.0161 | 0.0383 | 0.0197 | 0.0178 | 0.0378 | 0.0098 | 0.0168 | 0.0429 | 0.0435 | 0.0329 | 0.0367 | 0.025 | 0.040 | 0.0382 | 0.0339 | 0.0333 | 0.0468 | 0.0232 | 0.0408 | 0.0376 | 0.0391 | 0.038 | 0.0193 | 0.0441 | 0.0376 | 0.0437 | 0.047 | 0.0041 | 0.0443 | 0.0444 | 0.0406 | 0.0279 | 0.0409 | 0.0449 | 0.0478 | 0.0361 | 0.0406 | 0.0359 | 0.0231 | 0.0319 | 0.041 | 0.0062 | 0.0125 | 0.0161 | 0.0384 | 0.000 | 0.0038 | 0.002 | 0.002 | 0.000 | 0.0019 | 0.0061 | 0.006 | 0.004 | 0.000 | 0.008 | 0.0082 | 0.002 | 0.0041 | 0.0061 | 0.0061 | 0.004 | 0.0059 | 0.0348 | 0.0249 | 0.0277 | 0.0138 | 0.0142 | 0.0292 | 0.040 | 0.0193 | 0.0488 | 0.0307 | 0.0277 | 0.0357 | 0.0309 | 0.0408 | 0.048 | 0.046 | 0.0248 | 0.0472 | 0.0198 | 0.0202 | 0.0233 | 0.0435 | 0.0442 | 0.0239 | 0.0449 | 0.0253 | 0.0335 | 0.0431 | 0.0337 | 0.0422 | 0.0081 | 0.0498 | 0.0313 | 0.0364 | 0.0385 | 0.0452 | 0.0475 | 0.0167 | 0.0485 | 0.0354 |
enrichment_ratio_dcor <- NULL
enrichment_ratio_ttest <- NULL
for ( ii in 1:length(Significant_in_dcor_not_in_GSEA) ){
aux_genes <- intersect(pathway_collapsed[[Significant_in_dcor_not_in_GSEA[[ii]]]],colnames(expressions))
aux_pathway_dcor <- dcor.test(dist(expressions[,aux_genes]),dist(genotypes),R=10000)
aux_individual_genes_in_pathway_dcor <- sapply(aux_genes,function(x) dcor.test(dist(expressions[,x]),dist(genotypes),R=10000)$p.value<0.05 )
aux_enrichment_ratio_dcor <- sum(aux_individual_genes_in_pathway_dcor)/length(aux_individual_genes_in_pathway_dcor)
enrichment_ratio_dcor[ii] <- aux_enrichment_ratio_dcor
aux_individual_genes_in_pathway_ttest <- sapply(aux_genes,function(x) t.test(expressions[,x]~genotypes)$p.value<0.05 )
aux_enrichment_ratio_ttest <- sum(aux_individual_genes_in_pathway_ttest)/length(aux_individual_genes_in_pathway_ttest)
aux_enrichment_ratio_ttest
enrichment_ratio_ttest[ii] <-aux_enrichment_ratio_ttest
}
enrichment_ratio_comparison <- rbind(enrichment_ratio_dcor,enrichment_ratio_ttest)
rownames(enrichment_ratio_comparison) <- c("MPEA","GSEA")
colnames(enrichment_ratio_comparison) <- Significant_in_dcor_not_in_GSEA
enrichment_ratio_comparison%>%
kable("html", digits = 4, longtable = TRUE) %>%
kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
row_spec(0, angle = -0)
| KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP | HEIDENBLAD_AMPLICON_12P11_12_UP | MORI_SMALL_PRE_BII_LYMPHOCYTE_UP | SHEPARD_CRUSH_AND_BURN_MUTANT_UP | MA_MYELOID_DIFFERENTIATION_DN | ZHENG_FOXP3_TARGETS_IN_THYMUS_UP | LEE_DIFFERENTIATING_T_LYMPHOCYTE | WHITFIELD_CELL_CYCLE_G2 | CEBALLOS_TARGETS_OF_TP53_AND_MYC_UP | BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN | DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER | SMITH_TERT_TARGETS_DN | WANG_TARGETS_OF_MLL_CBP_FUSION_DN | ZHANG_TLX_TARGETS_60HR_DN | WIERENGA_STAT5A_TARGETS_UP | ENK_UV_RESPONSE_KERATINOCYTE_DN | FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN | FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP | FRIDMAN_IMMORTALIZATION_DN | GEORGES_TARGETS_OF_MIR192_AND_MIR215 | FOSTER_TOLERANT_MACROPHAGE_UP | WALLACE_PROSTATE_CANCER_RACE_UP | WATANABE_ULCERATIVE_COLITIS_WITH_CANCER_UP | WIERENGA_STAT5A_TARGETS_GROUP1 | BHAT_ESR1_TARGETS_VIA_AKT1_UP | FISCHER_DIRECT_P53_TARGETS_META_ANALYSIS | PID_PTP1B_PATHWAY | SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_UP | MITSIADES_RESPONSE_TO_APLIDIN_UP | PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7 | OISHI_CHOLANGIOMA_STEM_CELL_LIKE_DN | GARY_CD5_TARGETS_DN | CAFFAREL_RESPONSE_TO_THC_DN | OUILLETTE_CLL_13Q14_DELETION_DN | ENGELMANN_CANCER_PROGENITORS_DN | REACTOME_ABORTIVE_ELONGATION_OF_HIV1_TRANSCRIPT_IN_THE_ABSENCE_OF_TAT | HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_DN | IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_UP | BHAT_ESR1_TARGETS_NOT_VIA_AKT1_UP | KEGG_STEROID_BIOSYNTHESIS | KEGG_RNA_POLYMERASE | PID_EPHA_FWDPATHWAY | JAEGER_METASTASIS_DN | LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP | WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_DN | BIOCARTA_CARDIACEGF_PATHWAY | REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PI3KGAMMA | FORTSCHEGGER_PHF8_TARGETS_UP | LIU_PROSTATE_CANCER_UP | LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q | BROWNE_HCMV_INFECTION_48HR_UP | HORTON_SREBF_TARGETS | BIOCARTA_PAR1_PATHWAY | REACTOME_MICRORNA_MIRNA_BIOGENESIS | REACTOME_PI3K_AKT_ACTIVATION | REACTOME_FORMATION_OF_THE_HIV1_EARLY_ELONGATION_COMPLEX | BORCZUK_MALIGNANT_MESOTHELIOMA_UP | REACTOME_FORMATION_OF_TRANSCRIPTION_COUPLED_NER_TC_NER_REPAIR_COMPLEX | NAGASHIMA_NRG1_SIGNALING_DN | CHEBOTAEV_GR_TARGETS_DN | GEISS_RESPONSE_TO_DSRNA_DN | LABBE_WNT3A_TARGETS_DN | HELLEBREKERS_SILENCED_DURING_TUMOR_ANGIOGENESIS | KEGG_PYRIMIDINE_METABOLISM | FARMER_BREAST_CANCER_APOCRINE_VS_LUMINAL | MACLACHLAN_BRCA1_TARGETS_UP | QI_HYPOXIA_TARGETS_OF_HIF1A_AND_FOXA2 | PID_S1P_S1P2_PATHWAY | YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_5 | PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP | DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_DN | PID_LIS1_PATHWAY | REACTOME_REGULATORY_RNA_PATHWAYS | REACTOME_RNA_POL_II_TRANSCRIPTION_PRE_INITIATION_AND_PROMOTER_OPENING | REACTOME_GPVI_MEDIATED_ACTIVATION_CASCADE | SHI_SPARC_TARGETS_UP | ZHANG_ANTIVIRAL_RESPONSE_TO_RIBAVIRIN_DN | TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_UP | PLASARI_NFIC_TARGETS_BASAL_UP | PID_PRL_SIGNALING_EVENTS_PATHWAY | PID_S1P_S1P3_PATHWAY | PID_EPHA2_FWD_PATHWAY | HOUSTIS_ROS | ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_DN | PID_AVB3_INTEGRIN_PATHWAY | DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP | SANSOM_APC_TARGETS_DN | RAMPON_ENRICHED_LEARNING_ENVIRONMENT_LATE_UP | PID_ECADHERIN_KERATINOCYTE_PATHWAY | REACTOME_G_PROTEIN_BETA_GAMMA_SIGNALLING | PETROVA_PROX1_TARGETS_UP | BROWNE_HCMV_INFECTION_6HR_DN | CHEN_ETV5_TARGETS_TESTIS | NADLER_HYPERGLYCEMIA_AT_OBESITY | DAZARD_RESPONSE_TO_UV_NHEK_DN | WINNEPENNINCKX_MELANOMA_METASTASIS_DN | BIOCARTA_CDC42RAC_PATHWAY | PID_P53_REGULATION_PATHWAY | GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREY_DN | MULLIGHAN_NPM1_SIGNATURE_3_UP | SHEN_SMARCA2_TARGETS_UP | SA_TRKA_RECEPTOR | PID_TGFBR_PATHWAY | REACTOME_SEMA4D_IN_SEMAPHORIN_SIGNALING | PETRETTO_CARDIAC_HYPERTROPHY | ONDER_CDH1_TARGETS_1_UP | BILD_MYC_ONCOGENIC_SIGNATURE | RIGGI_EWING_SARCOMA_PROGENITOR_DN | PID_WNT_NONCANONICAL_PATHWAY | GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_DN | VERHAAK_GLIOBLASTOMA_NEURAL | KASLER_HDAC7_TARGETS_1_DN | PID_S1P_S1P1_PATHWAY | TARTE_PLASMA_CELL_VS_PLASMABLAST_DN | MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_DN | PLASARI_TGFB1_TARGETS_10HR_DN | REACTOME_RNA_POL_III_TRANSCRIPTION_TERMINATION | MENSE_HYPOXIA_UP | BOCHKIS_FOXA2_TARGETS | BIOCARTA_RAS_PATHWAY | PID_SYNDECAN_4_PATHWAY | REACTOME_RNA_POL_III_TRANSCRIPTION | MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP | MULLIGHAN_NPM1_MUTATED_SIGNATURE_2_UP | BERTUCCI_INVASIVE_CARCINOMA_DUCTAL_VS_LOBULAR_DN | GAJATE_RESPONSE_TO_TRABECTEDIN_UP | MARIADASON_RESPONSE_TO_CURCUMIN_SULINDAC_5 | COATES_MACROPHAGE_M1_VS_M2_DN | LIN_NPAS4_TARGETS_UP | REACTOME_G_ALPHA1213_SIGNALLING_EVENTS | FARMER_BREAST_CANCER_APOCRINE_VS_BASAL | JOHNSTONE_PARVB_TARGETS_3_UP | KENNY_CTNNB1_TARGETS_DN | BRACHAT_RESPONSE_TO_CAMPTOTHECIN_UP | WANG_SMARCE1_TARGETS_UP | LEIN_CHOROID_PLEXUS_MARKERS | BERNARD_PPAPDC1B_TARGETS_UP | BROWNE_HCMV_INFECTION_4HR_DN | MCBRYAN_PUBERTAL_TGFB1_TARGETS_DN | HU_ANGIOGENESIS_DN | SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY | NUYTTEN_NIPP1_TARGETS_UP | SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP | MURAKAMI_UV_RESPONSE_6HR_DN | BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN | BYSTRYKH_HEMATOPOIESIS_STEM_CELL_SCP2_QTL_TRANS | WIERENGA_STAT5A_TARGETS_GROUP2 | CASORELLI_APL_SECONDARY_VS_DE_NOVO_UP | BASAKI_YBX1_TARGETS_UP | RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP | MARTORIATI_MDM4_TARGETS_FETAL_LIVER_UP | LENAOUR_DENDRITIC_CELL_MATURATION_DN | WINZEN_DEGRADED_VIA_KHSRP | LIU_SOX4_TARGETS_UP | PENG_RAPAMYCIN_RESPONSE_UP | ACOSTA_PROLIFERATION_INDEPENDENT_MYC_TARGETS_UP | BIOCARTA_EDG1_PATHWAY | PID_ECADHERIN_NASCENT_AJ_PATHWAY | NOJIMA_SFRP2_TARGETS_UP | ODONNELL_METASTASIS_DN | LEE_TARGETS_OF_PTCH1_AND_SUFU_DN | UEDA_PERIFERAL_CLOCK | HASLINGER_B_CLL_WITH_MUTATED_VH_GENES | MCCLUNG_COCAINE_REWARD_5D | CADWELL_ATG16L1_TARGETS_DN | MIKKELSEN_ES_HCP_WITH_H3_UNMETHYLATED | LI_INDUCED_T_TO_NATURAL_KILLER_DN | GUILLAUMOND_KLF10_TARGETS_DN | BIOCARTA_PTDINS_PATHWAY | SAMOLS_TARGETS_OF_KHSV_MIRNAS_DN | MARKS_HDAC_TARGETS_UP | VANTVEER_BREAST_CANCER_ESR1_UP | GUTIERREZ_MULTIPLE_MYELOMA_UP | REACTOME_SEMA4D_INDUCED_CELL_MIGRATION_AND_GROWTH_CONE_COLLAPSE | REACTOME_CHOLESTEROL_BIOSYNTHESIS | ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP | RODWELL_AGING_KIDNEY_NO_BLOOD_DN | AMIT_EGF_RESPONSE_40_MCF10A | SCHLINGEMANN_SKIN_CARCINOGENESIS_TPA_UP | REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_2_PROMOTER | MOREIRA_RESPONSE_TO_TSA_UP | MURAKAMI_UV_RESPONSE_24HR | YAMASHITA_METHYLATED_IN_PROSTATE_CANCER | FONTAINE_THYROID_TUMOR_UNCERTAIN_MALIGNANCY_UP | GOLUB_ALL_VS_AML_DN | MASSARWEH_RESPONSE_TO_ESTRADIOL | BRUECKNER_TARGETS_OF_MIRLET7A3_UP | REACTOME_PEROXISOMAL_LIPID_METABOLISM | REACTOME_MRNA_SPLICING_MINOR_PATHWAY | VARELA_ZMPSTE24_TARGETS_UP | DE_YY1_TARGETS_UP | TIAN_TNF_SIGNALING_NOT_VIA_NFKB | HUANG_GATA2_TARGETS_UP | KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT | REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_3_PROMOTER | GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_UP | PUJANA_BRCA2_PCC_NETWORK | RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_DN | CUI_GLUCOSE_DEPRIVATION | BIOCARTA_RACCYCD_PATHWAY | GRAHAM_CML_DIVIDING_VS_NORMAL_QUIESCENT_DN | KEEN_RESPONSE_TO_ROSIGLITAZONE_UP | BURTON_ADIPOGENESIS_6 | COATES_MACROPHAGE_M1_VS_M2_UP | MANALO_HYPOXIA_DN | VERRECCHIA_EARLY_RESPONSE_TO_TGFB1 | SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_1 | AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_DN | REACTOME_P75_NTR_RECEPTOR_MEDIATED_SIGNALLING | MISSIAGLIA_REGULATED_BY_METHYLATION_UP | SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_DN | JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_UP | SCHMIDT_POR_TARGETS_IN_LIMB_BUD_UP | BIOCARTA_P53HYPOXIA_PATHWAY | PID_IL4_2PATHWAY | YAGI_AML_RELAPSE_PROGNOSIS | HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_DN | YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_1 | ODONNELL_TARGETS_OF_MYC_AND_TFRC_UP | RICKMAN_METASTASIS_UP | CUI_TCF21_TARGETS_DN | YAGI_AML_WITH_T_8_21_TRANSLOCATION | WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_UP | TERAMOTO_OPN_TARGETS_CLUSTER_7 | PETRETTO_HEART_MASS_QTL_CIS_DN | LAMB_CCND1_TARGETS | GENTILE_UV_LOW_DOSE_UP | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MPEA | 0.0826 | 0.0435 | 0.0968 | 0.064 | 0.0556 | 0.0310 | 0.0840 | 0.0294 | 0.0526 | 0.0541 | 0.0526 | 0.08 | 0.0667 | 0.0287 | 0.0365 | 0.0249 | 0.0504 | 0.0532 | 0.0645 | 0.0563 | 0.0566 | 0.0377 | 0.2000 | 0.0366 | 0.0517 | 0.0588 | 0.04 | 0.0581 | 0.0625 | 0.0437 | 0.0669 | 0.0361 | 0.0455 | 0.0513 | 0.0851 | 0.0870 | 0.0952 | 0.0476 | 0.0403 | 0.0625 | 0.1364 | 0.0667 | 0.0359 | 0.1333 | 0.0435 | 0.0588 | 0.05 | 0.0645 | 0.0667 | 0.0759 | 0.0327 | 0.0455 | 0.0571 | 0.10 | 0.0385 | 0.1250 | 0.0363 | 0.1481 | 0.150 | 0.0571 | 0.125 | 0.0649 | 0.0469 | 0.0541 | 0.0474 | 0.0588 | 0.0357 | 0.0909 | 0.12 | 0.0263 | 0.0386 | 0.12 | 0.10 | 0.1026 | 0.0333 | 0.0556 | 0.0217 | 0.0422 | 0.0952 | 0.1 | 0.0833 | 0.0588 | 0.0909 | 0.0263 | 0.0725 | 0.0398 | 0.0445 | 0.10 | 0.0526 | 0.087 | 0.087 | 0.0703 | 0.0556 | 0.0851 | 0.0302 | 0.0323 | 0.0625 | 0.0417 | 0.0278 | 0.0397 | 0.0390 | 0.0625 | 0.0408 | 0.0741 | 0.1034 | 0.0467 | 0.0256 | 0.0385 | 0.0357 | 0.0441 | 0.0654 | 0.1250 | 0.1053 | 0.0532 | 0.0385 | 0.0529 | 0.0625 | 0.0333 | 0.0648 | 0.0455 | 0.0333 | 0.0667 | 0.0296 | 0.0303 | 0.1111 | 0.1404 | 0.0476 | 0.02 | 0.1011 | 0.0492 | 0.0498 | 0.0569 | 0.0526 | 0.0526 | 0.0506 | 0.0429 | 0.0769 | 0.0343 | 0.1000 | 0.0938 | 0.1923 | 0.044 | 0.0633 | 0 | 0.0476 | 0.0556 | 0.0488 | 0.037 | 0.0309 | 0.0705 | 0.0645 | 0.0727 | 0.026 | 0.0421 | 0.0366 | 0.0469 | 0.0833 | 0.1351 | 0.0417 | 0.05 | 0.0508 | 0.0265 | 0.2353 | 0.0615 | 0.0732 | 0.0323 | 0.0875 | 0.0435 | 0.0455 | 0.0435 | 0.0526 | 0.0306 | 0.1034 | 0.087 | 0.05 | 0.0357 | 0.1010 | 0.0625 | 0.1786 | 0.05 | 0.1250 | 0.0556 | 0.0227 | 0.08 | 0.0556 | 0.0217 | 0.0267 | 0.125 | 0.0606 | 0.0312 | 0.1765 | 0.1053 | 0.1089 | 0.04 | 0.087 | 0.0172 | 0.0324 | 0.03 | 0.0612 | 0.0385 | 0.0238 | 0.08 | 0.0676 | 0.0612 | 0.0448 | 0.1176 | 0.0448 | 0.046 | 0.0455 | 0.0404 | 0.1351 | 0.2174 | 0.0455 | 0.0476 | 0.0345 | 0.069 | 0.087 | 0.0769 | 0.0909 | 0.0398 | 0.0909 | 0.0435 | 0.0854 | 0.0000 | 0.1250 | 0.0588 | 0.1053 |
| GSEA | 0.0642 | 0.0435 | 0.0806 | 0.048 | 0.0278 | 0.0388 | 0.0756 | 0.0392 | 0.1053 | 0.0473 | 0.0526 | 0.08 | 0.0667 | 0.0287 | 0.0438 | 0.0174 | 0.0570 | 0.0560 | 0.0645 | 0.0563 | 0.0660 | 0.0335 | 0.1333 | 0.0488 | 0.0460 | 0.0535 | 0.08 | 0.0465 | 0.0565 | 0.0397 | 0.0544 | 0.0289 | 0.0455 | 0.0513 | 0.0426 | 0.0435 | 0.0952 | 0.0381 | 0.0484 | 0.1250 | 0.0909 | 0.0667 | 0.0448 | 0.1000 | 0.0478 | 0.0588 | 0.10 | 0.0452 | 0.0833 | 0.0633 | 0.0261 | 0.0455 | 0.0857 | 0.05 | 0.0385 | 0.0938 | 0.0403 | 0.1111 | 0.125 | 0.0571 | 0.125 | 0.0779 | 0.0312 | 0.0405 | 0.0553 | 0.0588 | 0.0357 | 0.1364 | 0.12 | 0.0263 | 0.0429 | 0.08 | 0.05 | 0.1026 | 0.0333 | 0.0556 | 0.0652 | 0.0422 | 0.0476 | 0.1 | 0.1250 | 0.0588 | 0.0909 | 0.0789 | 0.0725 | 0.0398 | 0.0582 | 0.05 | 0.0526 | 0.087 | 0.087 | 0.0703 | 0.0556 | 0.0638 | 0.0345 | 0.0645 | 0.0625 | 0.0417 | 0.1111 | 0.0556 | 0.0496 | 0.0625 | 0.0204 | 0.0741 | 0.0345 | 0.0374 | 0.0342 | 0.0385 | 0.0714 | 0.0588 | 0.0374 | 0.0625 | 0.1053 | 0.0456 | 0.0769 | 0.0471 | 0.0625 | 0.0167 | 0.0648 | 0.0455 | 0.0333 | 0.0667 | 0.0443 | 0.0404 | 0.1389 | 0.1053 | 0.0476 | 0.02 | 0.0674 | 0.0656 | 0.0536 | 0.0569 | 0.0526 | 0.0526 | 0.0337 | 0.0429 | 0.0385 | 0.0294 | 0.0833 | 0.0625 | 0.0769 | 0.044 | 0.0367 | 0 | 0.0476 | 0.1111 | 0.0488 | 0.037 | 0.0309 | 0.0601 | 0.0323 | 0.0545 | 0.013 | 0.0421 | 0.0427 | 0.0469 | 0.0417 | 0.1081 | 0.0833 | 0.10 | 0.0508 | 0.0265 | 0.1765 | 0.0462 | 0.0732 | 0.0323 | 0.0875 | 0.0435 | 0.0455 | 0.0435 | 0.0526 | 0.0306 | 0.1034 | 0.087 | 0.10 | 0.1071 | 0.0707 | 0.0625 | 0.1071 | 0.05 | 0.0833 | 0.0000 | 0.1136 | 0.12 | 0.1667 | 0.0217 | 0.0267 | 0.125 | 0.0303 | 0.0312 | 0.1765 | 0.1053 | 0.0891 | 0.08 | 0.087 | 0.0345 | 0.0295 | 0.04 | 0.0612 | 0.0385 | 0.0357 | 0.08 | 0.0608 | 0.0816 | 0.0448 | 0.1373 | 0.0420 | 0.046 | 0.0606 | 0.0303 | 0.0811 | 0.1739 | 0.0909 | 0.0476 | 0.0517 | 0.069 | 0.087 | 0.0769 | 0.0909 | 0.0284 | 0.0909 | 0.0401 | 0.0610 | 0.0588 | 0.1875 | 0.0588 | 0.0526 |
t.test(enrichment_ratio_dcor,enrichment_ratio_ttest)
##
## Welch Two Sample t-test
##
## data: enrichment_ratio_dcor and enrichment_ratio_ttest
## t = 0.44538, df = 444.32, p-value = 0.6563
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -0.004944176 0.007841671
## sample estimates:
## mean of x mean of y
## 0.06485219 0.06340344
enrichment_ratios_percenages <- rbind(sum(enrichment_ratio_dcor>enrichment_ratio_ttest)/length(enrichment_ratio_dcor),
sum(enrichment_ratio_dcor<enrichment_ratio_ttest)/length(enrichment_ratio_dcor),
sum(enrichment_ratio_dcor==enrichment_ratio_ttest)/length(enrichment_ratio_dcor))*100
rownames(enrichment_ratios_percenages) <- c ( "More univariate enrichment detected in Dcor", "More univariate enrichment detected in T-test", "Draw" )
colnames(enrichment_ratios_percenages) <- "Percentage"
enrichment_ratios_percenages%>%
kable("html", digits = 4, longtable = TRUE) %>%
kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
row_spec(0, angle = -0)
| Percentage | |
|---|---|
| More univariate enrichment detected in Dcor | 33.4802 |
| More univariate enrichment detected in T-test | 25.9912 |
| Draw | 40.5286 |
enrichment_ratio_dcor <- NULL
enrichment_ratio_ttest <- NULL
for ( ii in 1:length(Significant_in_GSEA_not_in_dcor) ){
aux_genes <- intersect(pathway_collapsed[[Significant_in_GSEA_not_in_dcor[[ii]]]],colnames(expressions))
if ( identical(aux_genes, character(0))) next
aux_pathway_dcor <- dcor.test(dist(expressions[,aux_genes]),dist(genotypes),R=10000)
aux_individual_genes_in_pathway_dcor <- sapply(aux_genes,function(x) dcor.test(dist(expressions[,x]),dist(genotypes),R=10000)$p.value<0.05 )
aux_enrichment_ratio_dcor <- sum(aux_individual_genes_in_pathway_dcor)/length(aux_individual_genes_in_pathway_dcor)
enrichment_ratio_dcor[ii] <- aux_enrichment_ratio_dcor
aux_individual_genes_in_pathway_ttest <- sapply(aux_genes,function(x) t.test(expressions[,x]~genotypes)$p.value<0.05 )
aux_enrichment_ratio_ttest <- sum(aux_individual_genes_in_pathway_ttest)/length(aux_individual_genes_in_pathway_ttest)
aux_enrichment_ratio_ttest
enrichment_ratio_ttest[ii] <-aux_enrichment_ratio_ttest
}
enrichment_ratio_comparison <- rbind(enrichment_ratio_dcor,enrichment_ratio_ttest)
rownames(enrichment_ratio_comparison) <- c("MPEA","GSEA")
colnames(enrichment_ratio_comparison) <- Significant_in_GSEA_not_in_dcor
enrichment_ratio_comparison%>%
kable("html", digits = 4, longtable = TRUE) %>%
kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
row_spec(0, angle = -0)
| LUI_TARGETS_OF_PAX8_PPARG_FUSION | LUI_THYROID_CANCER_CLUSTER_3 | ANDERSEN_LIVER_CANCER_KRT19_UP | REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_ | POMEROY_MEDULLOBLASTOMA_PROGNOSIS_DN | MCBRYAN_PUBERTAL_BREAST_3_4WK_DN | REACTOME_INFLUENZA_LIFE_CYCLE | LANDIS_ERBB2_BREAST_TUMORS_324_UP | KEGG_ALZHEIMERS_DISEASE | REACTOME_METABOLISM_OF_RNA | CHNG_MULTIPLE_MYELOMA_HYPERPLOID_UP | REACTOME_RESPIRATORY_ELECTRON_TRANSPORT | FAELT_B_CLL_WITH_VH_REARRANGEMENTS_UP | REACTOME_DOWNREGULATION_OF_SMAD2_3_SMAD4_TRANSCRIPTIONAL_ACTIVITY | REACTOME_METABOLISM_OF_MRNA | PECE_MAMMARY_STEM_CELL_UP | KEGG_NUCLEOTIDE_EXCISION_REPAIR | TONG_INTERACT_WITH_PTTG1 | EHLERS_ANEUPLOIDY_UP | YAMASHITA_LIVER_CANCER_WITH_EPCAM_UP | KANNAN_TP53_TARGETS_DN | DUNNE_TARGETS_OF_AML1_MTG8_FUSION_DN | MEINHOLD_OVARIAN_CANCER_LOW_GRADE_DN | REACTOME_NONSENSE_MEDIATED_DECAY_ENHANCED_BY_THE_EXON_JUNCTION_COMPLEX | REACTOME_TRANSLATION | REACTOME_SYNTHESIS_AND_INTERCONVERSION_OF_NUCLEOTIDE_DI_AND_TRIPHOSPHATES | TAKAO_RESPONSE_TO_UVB_RADIATION_UP | BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_DN | REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE | HUMMERICH_BENIGN_SKIN_TUMOR_UP | HSIAO_HOUSEKEEPING_GENES | JAZAG_TGFB1_SIGNALING_UP | BAE_BRCA1_TARGETS_UP | KEGG_RIBOSOME | NUTT_GBM_VS_AO_GLIOMA_DN | MARTINEZ_RESPONSE_TO_TRABECTEDIN_UP | KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_DN | REACTOME_METABOLISM_OF_PROTEINS | BILANGES_SERUM_RESPONSE_TRANSLATION | LANDIS_BREAST_CANCER_PROGRESSION_UP | NAKAYAMA_FGF2_TARGETS | HUNSBERGER_EXERCISE_REGULATED_GENES | LUI_THYROID_CANCER_PAX8_PPARG_DN | WENG_POR_TARGETS_GLOBAL_UP | REACTOME_PEPTIDE_CHAIN_ELONGATION | NIKOLSKY_BREAST_CANCER_8P12_P11_AMPLICON | IRITANI_MAD1_TARGETS_DN | YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_17 | LEE_LIVER_CANCER_SURVIVAL_DN | REACTOME_SIGNAL_AMPLIFICATION | WANG_RESPONSE_TO_FORSKOLIN_UP | JIANG_AGING_HYPOTHALAMUS_UP | PARK_HSC_VS_MULTIPOTENT_PROGENITORS_DN | HOLLEMAN_ASPARAGINASE_RESISTANCE_ALL_UP | KEGG_BASAL_TRANSCRIPTION_FACTORS | OSMAN_BLADDER_CANCER_DN | YANG_BREAST_CANCER_ESR1_UP | ZHAN_MULTIPLE_MYELOMA_HP_UP | PARK_HSC_MARKERS | REACTOME_TGF_BETA_RECEPTOR_SIGNALING_ACTIVATES_SMADS | WANG_TUMOR_INVASIVENESS_UP | REACTOME_GLOBAL_GENOMIC_NER_GG_NER | GEORGES_CELL_CYCLE_MIR192_TARGETS | MAINA_VHL_TARGETS_DN | CHEN_PDGF_TARGETS | SCHRAMM_INHBA_TARGETS_DN | FAELT_B_CLL_WITH_VH3_21_DN | BOUDOUKHA_BOUND_BY_IGF2BP2 | NATSUME_RESPONSE_TO_INTERFERON_BETA_DN | REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE | GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN | MURAKAMI_UV_RESPONSE_1HR_UP | PID_PI3K_PLC_TRK_PATHWAY | REACTOME_ADP_SIGNALLING_THROUGH_P2RY1 | WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP | CHANGOLKAR_H2AFY_TARGETS_UP | BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_UP | PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_DN | BORLAK_LIVER_CANCER_EGF_UP | REACTOME_G_ALPHA_Z_SIGNALLING_EVENTS | YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9 | KIM_MYC_AMPLIFICATION_TARGETS_UP | LINDGREN_BLADDER_CANCER_CLUSTER_1_UP | CHANGOLKAR_H2AFY_TARGETS_DN | HORIUCHI_WTAP_TARGETS_DN | SASAKI_ADULT_T_CELL_LEUKEMIA | GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN | REACTOME_INTEGRATION_OF_ENERGY_METABOLISM | DELASERNA_MYOD_TARGETS_UP | KASLER_HDAC7_TARGETS_2_DN | PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_DN | SHIN_B_CELL_LYMPHOMA_CLUSTER_8 | DOANE_BREAST_CANCER_ESR1_DN | BIOCARTA_AGR_PATHWAY | REACTOME_RNA_POL_I_PROMOTER_OPENING | REACTOME_HDL_MEDIATED_LIPID_TRANSPORT | FAELT_B_CLL_WITH_VH3_21_UP | KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3 | HASLINGER_B_CLL_WITH_6Q21_DELETION | KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_DN | KEGG_PPAR_SIGNALING_PATHWAY | REACTOME_DEPOSITION_OF_NEW_CENPA_CONTAINING_NUCLEOSOMES_AT_THE_CENTROMERE | MIKKELSEN_MEF_LCP_WITH_H3K27ME3 | XU_GH1_EXOGENOUS_TARGETS_DN | ABE_VEGFA_TARGETS_2HR | FIGUEROA_AML_METHYLATION_CLUSTER_1_DN | REACTOME_LIPOPROTEIN_METABOLISM | BONOME_OVARIAN_CANCER_POOR_SURVIVAL_DN | BIOCARTA_UCALPAIN_PATHWAY | ST_T_CELL_SIGNAL_TRANSDUCTION | DING_LUNG_CANCER_MUTATED_SIGNIFICANTLY | HUMMERICH_MALIGNANT_SKIN_TUMOR_DN | CHEMELLO_SOLEUS_VS_EDL_MYOFIBERS_UP | PID_NCADHERIN_PATHWAY | HUMMERICH_BENIGN_SKIN_TUMOR_DN | REACTOME_PACKAGING_OF_TELOMERE_ENDS | LEI_HOXC8_TARGETS_DN | PID_BARD1_PATHWAY | FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_UP | BIOCARTA_MAL_PATHWAY | XU_AKT1_TARGETS_6HR | PID_INSULIN_GLUCOSE_PATHWAY | REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS | SA_B_CELL_RECEPTOR_COMPLEXES | SCHEIDEREIT_IKK_INTERACTING_PROTEINS | REACTOME_BILE_ACID_AND_BILE_SALT_METABOLISM | ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_DN | BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_UP | RIZ_ERYTHROID_DIFFERENTIATION_HEMGN | MEISSNER_BRAIN_HCP_WITH_H3K27ME3 | REACTOME_SEMAPHORIN_INTERACTIONS | KUMAR_AUTOPHAGY_NETWORK | SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_DN | KENNY_CTNNB1_TARGETS_UP | OXFORD_RALA_OR_RALB_TARGETS_UP | LABBE_TARGETS_OF_TGFB1_AND_WNT3A_UP | MIKKELSEN_NPC_HCP_WITH_H3K27ME3 | BIOCARTA_HER2_PATHWAY | FIGUEROA_AML_METHYLATION_CLUSTER_3_DN | KYNG_DNA_DAMAGE_BY_4NQO | MULLIGHAN_NPM1_SIGNATURE_3_DN | PID_IL23_PATHWAY | REACTOME_MEIOTIC_RECOMBINATION | MIKKELSEN_MCV6_HCP_WITH_H3K27ME3 | CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP | QI_HYPOXIA | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MPEA | 0.0417 | 0.0000 | 0.0714 | 0.1972 | 0.0732 | 0.1290 | 0.0630 | 0.0467 | 0.1250 | 0.0509 | 0.0682 | 0.1636 | 0.0556 | 0 | 0.0546 | 0.0721 | 0.0476 | 0.1379 | 0.069 | 0.0222 | 0.0000 | 0.0000 | 0.2105 | 0.0625 | 0.0565 | 0.0625 | 0.0400 | 0.0833 | 0.0707 | 0.0000 | 0.0557 | 0.0549 | 0.0303 | 0.0732 | 0.0571 | 0.1404 | 0 | 0.0500 | 0.0385 | 0 | 0.0952 | 0.0333 | 0.0000 | 0 | 0.0741 | 0.0606 | 0.0323 | 0.0687 | 0.0703 | 0.04 | 0.0667 | 0.100 | 0 | 0.0000 | 0.0333 | 0.0490 | 0.0000 | 0.0294 | 0.0312 | 0.0435 | 0.0463 | 0.0625 | 0.08 | 0.0625 | 0 | 0 | 0.05 | 0.0811 | 0.0435 | 0.0538 | 0.0625 | 0.2667 | 0 | 0.0 | 0.0444 | 0.0455 | 0.0417 | 0.0714 | 0.0962 | 0.0811 | 0.0182 | 0.0758 | 0.0610 | 0.0769 | 0.0481 | 0.0470 | 0.0525 | 0.0737 | 0.0423 | 0.0476 | 0.0556 | 0.0645 | 0.0909 | 0.1515 | 0.0233 | 0.3333 | 0.0556 | 0.0588 | 0.0588 | 0.0617 | 0.0508 | 0.0270 | 0.0000 | 0.0125 | 0 | 0.0741 | 0.2500 | 0 | 0.1333 | 0.0698 | 0.08 | 0.1333 | 0.0345 | 0.0323 | 0.125 | 0.0294 | 0 | 0.0385 | 0.1111 | 0.0556 | 0.0476 | 0.1739 | 0.0625 | 0.0000 | 0 | 0.0833 | 0.0484 | 0 | 0.04 | 0.0244 | 0.0862 | 0.0732 | 0.1250 | 0.0682 | 0.1053 | 0.0215 | 0.0464 | 0.0455 | 0.0000 | 0.0645 | 0.0382 | 0.0000 | 0.0156 | 0.0345 | 0.0957 | 0.0495 |
| GSEA | 0.0833 | 0.0526 | 0.1071 | 0.1408 | 0.0732 | 0.0968 | 0.0787 | 0.0467 | 0.1103 | 0.0602 | 0.0682 | 0.1273 | 0.1111 | 0 | 0.0656 | 0.0631 | 0.0714 | 0.1379 | 0.069 | 0.0444 | 0.0526 | 0.0625 | 0.1579 | 0.0833 | 0.0726 | 0.0625 | 0.0267 | 0.1250 | 0.0909 | 0.0667 | 0.0645 | 0.0549 | 0.0303 | 0.0976 | 0.0571 | 0.0702 | 0 | 0.0533 | 0.0385 | 0 | 0.1429 | 0.0667 | 0.0312 | 0 | 0.0988 | 0.0606 | 0.0323 | 0.0611 | 0.0625 | 0.12 | 0.0667 | 0.125 | 0 | 0.0667 | 0.0667 | 0.0571 | 0.0303 | 0.0294 | 0.0312 | 0.0000 | 0.0320 | 0.0625 | 0.08 | 0.0000 | 0 | 0 | 0.05 | 0.0946 | 0.0652 | 0.0538 | 0.0417 | 0.2000 | 0 | 0.1 | 0.0222 | 0.0000 | 0.0833 | 0.0476 | 0.0769 | 0.0541 | 0.0364 | 0.0833 | 0.0854 | 0.1154 | 0.0385 | 0.0201 | 0.0612 | 0.0526 | 0.0282 | 0.0476 | 0.0000 | 0.0645 | 0.0682 | 0.1515 | 0.0465 | 0.3333 | 0.1111 | 0.0588 | 0.0588 | 0.0741 | 0.0678 | 0.0541 | 0.0294 | 0.0250 | 0 | 0.1111 | 0.2083 | 0 | 0.1333 | 0.0698 | 0.08 | 0.1333 | 0.0345 | 0.0323 | 0.125 | 0.0588 | 0 | 0.0385 | 0.0556 | 0.0556 | 0.0476 | 0.1304 | 0.0625 | 0.0833 | 0 | 0.0833 | 0.0806 | 0 | 0.00 | 0.0427 | 0.0862 | 0.0732 | 0.2083 | 0.0682 | 0.1053 | 0.0323 | 0.0515 | 0.0455 | 0.0435 | 0.0968 | 0.0534 | 0.0625 | 0.0312 | 0.0383 | 0.0696 | 0.0396 |
t.test(enrichment_ratio_dcor,enrichment_ratio_ttest)
##
## Welch Two Sample t-test
##
## data: enrichment_ratio_dcor and enrichment_ratio_ttest
## t = -1.0208, df = 287.16, p-value = 0.3082
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -0.017581364 0.005572975
## sample estimates:
## mean of x mean of y
## 0.05955527 0.06555946
enrichment_ratios_percenages <- rbind(sum(enrichment_ratio_dcor>enrichment_ratio_ttest,na.rm = T)/length(enrichment_ratio_dcor),
sum(enrichment_ratio_dcor<enrichment_ratio_ttest,na.rm = T)/length(enrichment_ratio_dcor),
sum(enrichment_ratio_dcor==enrichment_ratio_ttest,na.rm = T)/length(enrichment_ratio_dcor))*100
rownames(enrichment_ratios_percenages) <- c ( "More univariate enrichment detected in Dcor", "More univariate enrichment detected in T-test", "Draw" )
colnames(enrichment_ratios_percenages) <- "Percentage"
enrichment_ratios_percenages%>%
kable("html", digits = 4, longtable = TRUE) %>%
kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
row_spec(0, angle = -0)
| Percentage | |
|---|---|
| More univariate enrichment detected in Dcor | 21.9178 |
| More univariate enrichment detected in T-test | 40.4110 |
| Draw | 37.6712 |
# stopCluster(cl)
library(ggfortify)
## Loading required package: ggplot2
for (name in (sort(Significant_in_dcor_not_in_GSEA, decreasing = F))){
strongestpathwaydcor <- unname(unlist(pathway_collapsed[name]))
expressions_pathway <- as.data.frame(expressions[,which(colnames(expressions)%in% strongestpathwaydcor)])
genotypes_category <- ifelse(genotypes==1, "MUT", "WT")
genotypes_category <- as.data.frame(genotypes_category)
print(name)
print(autoplot(prcomp(expressions_pathway), data = genotypes_category, colour='genotypes_category' )+theme_bw()+ggtitle(label = "name"))
# pcoa.obj <- pcoa(D = dist(expressions_pathway), correction="none", rn=NULL)
# biplot.pcoa(pcoa.obj)
}
## [1] "ACOSTA_PROLIFERATION_INDEPENDENT_MYC_TARGETS_UP"
## [1] "AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_DN"
## [1] "AMIT_EGF_RESPONSE_40_MCF10A"
## [1] "BASAKI_YBX1_TARGETS_UP"
## [1] "BERNARD_PPAPDC1B_TARGETS_UP"
## [1] "BERTUCCI_INVASIVE_CARCINOMA_DUCTAL_VS_LOBULAR_DN"
## [1] "BHAT_ESR1_TARGETS_NOT_VIA_AKT1_UP"
## [1] "BHAT_ESR1_TARGETS_VIA_AKT1_UP"
## [1] "BILD_MYC_ONCOGENIC_SIGNATURE"
## [1] "BIOCARTA_CARDIACEGF_PATHWAY"
## [1] "BIOCARTA_CDC42RAC_PATHWAY"
## [1] "BIOCARTA_EDG1_PATHWAY"
## [1] "BIOCARTA_P53HYPOXIA_PATHWAY"
## [1] "BIOCARTA_PAR1_PATHWAY"
## [1] "BIOCARTA_PTDINS_PATHWAY"
## [1] "BIOCARTA_RACCYCD_PATHWAY"
## [1] "BIOCARTA_RAS_PATHWAY"
## [1] "BOCHKIS_FOXA2_TARGETS"
## [1] "BORCZUK_MALIGNANT_MESOTHELIOMA_UP"
## [1] "BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN"
## [1] "BRACHAT_RESPONSE_TO_CAMPTOTHECIN_UP"
## [1] "BROWNE_HCMV_INFECTION_48HR_UP"
## [1] "BROWNE_HCMV_INFECTION_4HR_DN"
## [1] "BROWNE_HCMV_INFECTION_6HR_DN"
## [1] "BRUECKNER_TARGETS_OF_MIRLET7A3_UP"
## [1] "BURTON_ADIPOGENESIS_6"
## [1] "BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN"
## [1] "BYSTRYKH_HEMATOPOIESIS_STEM_CELL_SCP2_QTL_TRANS"
## [1] "CADWELL_ATG16L1_TARGETS_DN"
## [1] "CAFFAREL_RESPONSE_TO_THC_DN"
## [1] "CASORELLI_APL_SECONDARY_VS_DE_NOVO_UP"
## [1] "CEBALLOS_TARGETS_OF_TP53_AND_MYC_UP"
## [1] "CHEBOTAEV_GR_TARGETS_DN"
## [1] "CHEN_ETV5_TARGETS_TESTIS"
## [1] "COATES_MACROPHAGE_M1_VS_M2_DN"
## [1] "COATES_MACROPHAGE_M1_VS_M2_UP"
## [1] "CUI_GLUCOSE_DEPRIVATION"
## [1] "CUI_TCF21_TARGETS_DN"
## [1] "DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP"
## [1] "DAZARD_RESPONSE_TO_UV_NHEK_DN"
## [1] "DE_YY1_TARGETS_UP"
## [1] "DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_DN"
## [1] "DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER"
## [1] "ENGELMANN_CANCER_PROGENITORS_DN"
## [1] "ENK_UV_RESPONSE_KERATINOCYTE_DN"
## [1] "FARMER_BREAST_CANCER_APOCRINE_VS_BASAL"
## [1] "FARMER_BREAST_CANCER_APOCRINE_VS_LUMINAL"
## [1] "FISCHER_DIRECT_P53_TARGETS_META_ANALYSIS"
## [1] "FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN"
## [1] "FONTAINE_THYROID_TUMOR_UNCERTAIN_MALIGNANCY_UP"
## [1] "FORTSCHEGGER_PHF8_TARGETS_UP"
## [1] "FOSTER_TOLERANT_MACROPHAGE_UP"
## [1] "FRIDMAN_IMMORTALIZATION_DN"
## [1] "FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP"
## [1] "GAJATE_RESPONSE_TO_TRABECTEDIN_UP"
## [1] "GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREY_DN"
## [1] "GARY_CD5_TARGETS_DN"
## [1] "GEISS_RESPONSE_TO_DSRNA_DN"
## [1] "GENTILE_UV_LOW_DOSE_UP"
## [1] "GEORGES_TARGETS_OF_MIR192_AND_MIR215"
## [1] "GOLUB_ALL_VS_AML_DN"
## [1] "GRAHAM_CML_DIVIDING_VS_NORMAL_QUIESCENT_DN"
## [1] "GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_UP"
## [1] "GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_DN"
## [1] "GUILLAUMOND_KLF10_TARGETS_DN"
## [1] "GUTIERREZ_MULTIPLE_MYELOMA_UP"
## [1] "HASLINGER_B_CLL_WITH_MUTATED_VH_GENES"
## [1] "HEIDENBLAD_AMPLICON_12P11_12_UP"
## [1] "HELLEBREKERS_SILENCED_DURING_TUMOR_ANGIOGENESIS"
## [1] "HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_DN"
## [1] "HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_DN"
## [1] "HORTON_SREBF_TARGETS"
## [1] "HOUSTIS_ROS"
## [1] "HU_ANGIOGENESIS_DN"
## [1] "HUANG_GATA2_TARGETS_UP"
## [1] "ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_DN"
## [1] "IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_UP"
## [1] "JAEGER_METASTASIS_DN"
## [1] "JOHNSTONE_PARVB_TARGETS_3_UP"
## [1] "JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_UP"
## [1] "KASLER_HDAC7_TARGETS_1_DN"
## [1] "KEEN_RESPONSE_TO_ROSIGLITAZONE_UP"
## [1] "KEGG_PYRIMIDINE_METABOLISM"
## [1] "KEGG_RNA_POLYMERASE"
## [1] "KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT"
## [1] "KEGG_STEROID_BIOSYNTHESIS"
## [1] "KENNY_CTNNB1_TARGETS_DN"
## [1] "KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP"
## [1] "LABBE_WNT3A_TARGETS_DN"
## [1] "LAMB_CCND1_TARGETS"
## [1] "LEE_DIFFERENTIATING_T_LYMPHOCYTE"
## [1] "LEE_TARGETS_OF_PTCH1_AND_SUFU_DN"
## [1] "LEIN_CHOROID_PLEXUS_MARKERS"
## [1] "LENAOUR_DENDRITIC_CELL_MATURATION_DN"
## [1] "LI_INDUCED_T_TO_NATURAL_KILLER_DN"
## [1] "LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP"
## [1] "LIN_NPAS4_TARGETS_UP"
## [1] "LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q"
## [1] "LIU_PROSTATE_CANCER_UP"
## [1] "LIU_SOX4_TARGETS_UP"
## [1] "MA_MYELOID_DIFFERENTIATION_DN"
## [1] "MACLACHLAN_BRCA1_TARGETS_UP"
## [1] "MANALO_HYPOXIA_DN"
## [1] "MARIADASON_RESPONSE_TO_CURCUMIN_SULINDAC_5"
## [1] "MARKS_HDAC_TARGETS_UP"
## [1] "MARTORIATI_MDM4_TARGETS_FETAL_LIVER_UP"
## [1] "MASSARWEH_RESPONSE_TO_ESTRADIOL"
## [1] "MCBRYAN_PUBERTAL_TGFB1_TARGETS_DN"
## [1] "MCCLUNG_COCAINE_REWARD_5D"
## [1] "MENSE_HYPOXIA_UP"
## [1] "MIKKELSEN_ES_HCP_WITH_H3_UNMETHYLATED"
## [1] "MISSIAGLIA_REGULATED_BY_METHYLATION_UP"
## [1] "MITSIADES_RESPONSE_TO_APLIDIN_UP"
## [1] "MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_DN"
## [1] "MOREIRA_RESPONSE_TO_TSA_UP"
## [1] "MORI_SMALL_PRE_BII_LYMPHOCYTE_UP"
## [1] "MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP"
## [1] "MULLIGHAN_NPM1_MUTATED_SIGNATURE_2_UP"
## [1] "MULLIGHAN_NPM1_SIGNATURE_3_UP"
## [1] "MURAKAMI_UV_RESPONSE_24HR"
## [1] "MURAKAMI_UV_RESPONSE_6HR_DN"
## [1] "NADLER_HYPERGLYCEMIA_AT_OBESITY"
## [1] "NAGASHIMA_NRG1_SIGNALING_DN"
## [1] "NOJIMA_SFRP2_TARGETS_UP"
## [1] "NUYTTEN_NIPP1_TARGETS_UP"
## [1] "ODONNELL_METASTASIS_DN"
## [1] "ODONNELL_TARGETS_OF_MYC_AND_TFRC_UP"
## [1] "OISHI_CHOLANGIOMA_STEM_CELL_LIKE_DN"
## [1] "ONDER_CDH1_TARGETS_1_UP"
## [1] "OUILLETTE_CLL_13Q14_DELETION_DN"
## [1] "PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7"
## [1] "PENG_RAPAMYCIN_RESPONSE_UP"
## [1] "PETRETTO_CARDIAC_HYPERTROPHY"
## [1] "PETRETTO_HEART_MASS_QTL_CIS_DN"
## [1] "PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP"
## [1] "PETROVA_PROX1_TARGETS_UP"
## [1] "PID_AVB3_INTEGRIN_PATHWAY"
## [1] "PID_ECADHERIN_KERATINOCYTE_PATHWAY"
## [1] "PID_ECADHERIN_NASCENT_AJ_PATHWAY"
## [1] "PID_EPHA_FWDPATHWAY"
## [1] "PID_EPHA2_FWD_PATHWAY"
## [1] "PID_IL4_2PATHWAY"
## [1] "PID_LIS1_PATHWAY"
## [1] "PID_P53_REGULATION_PATHWAY"
## [1] "PID_PRL_SIGNALING_EVENTS_PATHWAY"
## [1] "PID_PTP1B_PATHWAY"
## [1] "PID_S1P_S1P1_PATHWAY"
## [1] "PID_S1P_S1P2_PATHWAY"
## [1] "PID_S1P_S1P3_PATHWAY"
## [1] "PID_SYNDECAN_4_PATHWAY"
## [1] "PID_TGFBR_PATHWAY"
## [1] "PID_WNT_NONCANONICAL_PATHWAY"
## [1] "PLASARI_NFIC_TARGETS_BASAL_UP"
## [1] "PLASARI_TGFB1_TARGETS_10HR_DN"
## [1] "PUJANA_BRCA2_PCC_NETWORK"
## [1] "QI_HYPOXIA_TARGETS_OF_HIF1A_AND_FOXA2"
## [1] "RAMPON_ENRICHED_LEARNING_ENVIRONMENT_LATE_UP"
## [1] "RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_DN"
## [1] "REACTOME_ABORTIVE_ELONGATION_OF_HIV1_TRANSCRIPT_IN_THE_ABSENCE_OF_TAT"
## [1] "REACTOME_CHOLESTEROL_BIOSYNTHESIS"
## [1] "REACTOME_FORMATION_OF_THE_HIV1_EARLY_ELONGATION_COMPLEX"
## [1] "REACTOME_FORMATION_OF_TRANSCRIPTION_COUPLED_NER_TC_NER_REPAIR_COMPLEX"
## [1] "REACTOME_G_ALPHA1213_SIGNALLING_EVENTS"
## [1] "REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PI3KGAMMA"
## [1] "REACTOME_G_PROTEIN_BETA_GAMMA_SIGNALLING"
## [1] "REACTOME_GPVI_MEDIATED_ACTIVATION_CASCADE"
## [1] "REACTOME_MICRORNA_MIRNA_BIOGENESIS"
## [1] "REACTOME_MRNA_SPLICING_MINOR_PATHWAY"
## [1] "REACTOME_P75_NTR_RECEPTOR_MEDIATED_SIGNALLING"
## [1] "REACTOME_PEROXISOMAL_LIPID_METABOLISM"
## [1] "REACTOME_PI3K_AKT_ACTIVATION"
## [1] "REACTOME_REGULATORY_RNA_PATHWAYS"
## [1] "REACTOME_RNA_POL_II_TRANSCRIPTION_PRE_INITIATION_AND_PROMOTER_OPENING"
## [1] "REACTOME_RNA_POL_III_TRANSCRIPTION"
## [1] "REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_2_PROMOTER"
## [1] "REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_3_PROMOTER"
## [1] "REACTOME_RNA_POL_III_TRANSCRIPTION_TERMINATION"
## [1] "REACTOME_SEMA4D_IN_SEMAPHORIN_SIGNALING"
## [1] "REACTOME_SEMA4D_INDUCED_CELL_MIGRATION_AND_GROWTH_CONE_COLLAPSE"
## [1] "RICKMAN_METASTASIS_UP"
## [1] "RIGGI_EWING_SARCOMA_PROGENITOR_DN"
## [1] "RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP"
## [1] "RODWELL_AGING_KIDNEY_NO_BLOOD_DN"
## [1] "ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP"
## [1] "SA_TRKA_RECEPTOR"
## [1] "SAMOLS_TARGETS_OF_KHSV_MIRNAS_DN"
## [1] "SANSOM_APC_TARGETS_DN"
## [1] "SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_1"
## [1] "SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_UP"
## [1] "SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP"
## [1] "SCHLINGEMANN_SKIN_CARCINOGENESIS_TPA_UP"
## [1] "SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY"
## [1] "SCHMIDT_POR_TARGETS_IN_LIMB_BUD_UP"
## [1] "SHEN_SMARCA2_TARGETS_UP"
## [1] "SHEPARD_CRUSH_AND_BURN_MUTANT_UP"
## [1] "SHI_SPARC_TARGETS_UP"
## [1] "SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_DN"
## [1] "SMITH_TERT_TARGETS_DN"
## [1] "TARTE_PLASMA_CELL_VS_PLASMABLAST_DN"
## [1] "TERAMOTO_OPN_TARGETS_CLUSTER_7"
## [1] "TIAN_TNF_SIGNALING_NOT_VIA_NFKB"
## [1] "TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_UP"
## [1] "UEDA_PERIFERAL_CLOCK"
## [1] "VANTVEER_BREAST_CANCER_ESR1_UP"
## [1] "VARELA_ZMPSTE24_TARGETS_UP"
## [1] "VERHAAK_GLIOBLASTOMA_NEURAL"
## [1] "VERRECCHIA_EARLY_RESPONSE_TO_TGFB1"
## [1] "WALLACE_PROSTATE_CANCER_RACE_UP"
## [1] "WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_UP"
## [1] "WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_DN"
## [1] "WANG_SMARCE1_TARGETS_UP"
## [1] "WANG_TARGETS_OF_MLL_CBP_FUSION_DN"
## [1] "WATANABE_ULCERATIVE_COLITIS_WITH_CANCER_UP"
## [1] "WHITFIELD_CELL_CYCLE_G2"
## [1] "WIERENGA_STAT5A_TARGETS_GROUP1"
## [1] "WIERENGA_STAT5A_TARGETS_GROUP2"
## [1] "WIERENGA_STAT5A_TARGETS_UP"
## [1] "WINNEPENNINCKX_MELANOMA_METASTASIS_DN"
## [1] "WINZEN_DEGRADED_VIA_KHSRP"
## [1] "YAGI_AML_RELAPSE_PROGNOSIS"
## [1] "YAGI_AML_WITH_T_8_21_TRANSLOCATION"
## [1] "YAMASHITA_METHYLATED_IN_PROSTATE_CANCER"
## [1] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_1"
## [1] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_5"
## [1] "ZHANG_ANTIVIRAL_RESPONSE_TO_RIBAVIRIN_DN"
## [1] "ZHANG_TLX_TARGETS_60HR_DN"
## [1] "ZHENG_FOXP3_TARGETS_IN_THYMUS_UP"
# rownames(gsea_results_significant)
# for (name in (Significant_in_GSEA_not_in_dcor)){
# strongestpathwaydcor <- unname(unlist(pathway_collapsed[name]))
# expressions_pathway <- as.data.frame(expressions[,which(colnames(expressions)%in% strongestpathwaydcor)])
# genotypes_category <- ifelse(genotypes==1, "MUT", "WT")
# genotypes_category <- as.data.frame(genotypes_category)
# print(name)
# print(autoplot(prcomp(expressions_pathway), data = genotypes_category, colour='genotypes_category' )+theme_bw()+ggtitle(label = "name"))
#
# # pcoa.obj <- pcoa(D = dist(expressions_pathway), correction="none", rn=NULL)
# # biplot.pcoa(pcoa.obj)
# }